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Yorodumi- PDB-1lo8: X-ray crystal structure of 4-hydroxybenzoyl CoA thioesterase comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lo8 | ||||||
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Title | X-ray crystal structure of 4-hydroxybenzoyl CoA thioesterase complexed with 4-hydroxybenzyl CoA | ||||||
Components | 4-hydroxybenzoyl-CoA Thioesterase | ||||||
Keywords | HYDROLASE / Thioesterase / hot dog fold / catalytic mechanism | ||||||
Function / homology | Function and homology information 4-hydroxybenzoyl-CoA thioesterase / 4-hydroxybenzoyl-CoA thioesterase activity Similarity search - Function | ||||||
Biological species | Pseudomonas sp. CBS3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Thoden, J.B. / Holden, H.M. / Zhuang, Z. / Dunaway-Mariano, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: X-ray crystallographic analyses of inhibitor and substrate complexes of wild-type and mutant 4-hydroxybenzoyl-CoA thioesterase. Authors: Thoden, J.B. / Holden, H.M. / Zhuang, Z. / Dunaway-Mariano, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lo8.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lo8.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 1lo8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1lo8 ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1lo8 | HTTPS FTP |
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-Related structure data
Related structure data | 1lo7C 1lo9C 1bvqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assemble is a homotetramer. The independent monomer in the crystallographic independent unit sits on 222 site symmetry. Matrices to generage the tetramer are as follows: (1) -1 0 0 0 -1 0 0 0 1 49.4 0.0 0.0 (2) -1 0 0 0 1 0 0 0 -1 49.4 0.0 0.0 (3) 1 0 0 0 -1 0 0 0 -1 0.0 0.0 0.0 |
-Components
#1: Protein | Mass: 16140.452 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. CBS3 (bacteria) / Strain: CBS-3 / Gene: 4HBT_PSESP / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: P56653, 4-hydroxybenzoyl-CoA thioesterase |
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#2: Chemical | ChemComp-4CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: batch / pH: 5 Details: PEG 8000, potassium chloride, succinate, 4-hydroxybenzyl CoA, pH 5.0, batch at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: sparse matrix screening | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Nov 8, 2001 / Details: goebel mirrors |
Radiation | Monochromator: goebel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 11789 / Num. obs: 11789 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.051 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1352 / Rsym value: 0.261 / % possible all: 91.2 |
Reflection | *PLUS Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 91.2 % / Num. unique obs: 1352 / Rmerge(I) obs: 0.261 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BVQ Resolution: 1.8→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Refinement | *PLUS Num. reflection obs: 10610 / Rfactor all: 0.193 / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.192 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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